STACK: Sequence Tag Alignment and Consensus Knowledgebase.

1South African National Bioinformatics Institute, Private Bag X17, Bellville 7535, University of Western Cape, South Africa.

Abstract

STACK is a tool for detection and visualisation of expressed transcript variation in the context of developmental and pathological states. The datasystem organizes and reconstructs human transcripts from available public data in the context of expression state. The expression state of a transcript can include developmental state, pathological association, site of expression and isoform of expressed transcript. STACK consensus transcripts are reconstructed from clusters that capture and reflect the growing evidence of transcript diversity. The comprehensive capture of transcript variants is achieved by the use of a novel clustering approach that is tolerant of sub-sequence diversity and does not rely on pairwise alignment. This is in contrast with other gene indexing projects. STACK is generated at least four times a year and represents the exhaustive processing of all publicly available human EST data extracted from GenBank. This processed information can be explored through 15 tissue-specific categories, a disease-related category and a whole-body index and is accessible via WWW at http://www.sanbi.ac.za/Dbases.html. STACK represents a broadly applicable resource, as it is the only reconstructed transcript database for which the tools for its generation are also broadly available (http://www.sanbi.ac.za/CODES).

An example linked entry for the olfactory tissue. The clusters contributing to the linked entry are displayed together with the ESTs comprising each cluster. A mouse click on a specific clusterID executes the download of the FASTA formatted multi-sequence file. The hyperlinks to the right of the clusterID provides for the display of detailed information pertaining to a cluster such as phrap alignments, consensus sequence and assembly analysis information. UniGene links to each EST are provided if they exist.